Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000893.1 Hibiscus syriacus cultivar Beakdansim tig00001750_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 734264
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 1 of 3
Found at i:117 original size:24 final size:24
Alignment explanation
Indices: 73--119 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
63 AAAAAGAACC
*
73 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
97 AAAATAAAGTTCAAACA-ACCATT
1 AAAATAAACTT-AAACATACCATT
120 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.57, C:0.15, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:3379 original size:19 final size:19
Alignment explanation
Indices: 3357--3399 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
3347 AGAAAAAGGT
3357 AAAAGTTAAAATGAAAGAG
1 AAAAGTTAAAATGAAAGAG
* * *
3376 AAAAATTAATATGAAAGAT
1 AAAAGTTAAAATGAAAGAG
3395 AAAAG
1 AAAAG
3400 AAAAAGTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.16, T:0.19
Consensus pattern (19 bp):
AAAAGTTAAAATGAAAGAG
Found at i:10160 original size:24 final size:24
Alignment explanation
Indices: 10116--10162 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
10106 ATAAAGAACC
*
10116 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
10140 AAAATAAAGTTCAAACA-ACCATT
1 AAAATAAACTT-AAACATACCATT
10163 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.57, C:0.15, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:11538 original size:2 final size:2
Alignment explanation
Indices: 11531--11557 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11521 ATATTTCAAA
11531 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
11558 CTGTAACACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12099 original size:21 final size:21
Alignment explanation
Indices: 12075--12123 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
12065 ACATATATCG
* *
12075 TCATCTATTTTCTTAGCATTA
1 TCATCTATATTATTAGCATTA
* *
12096 TCATATATATTATTATCATTA
1 TCATCTATATTATTAGCATTA
12117 TC-TCTAT
1 TCATCTAT
12124 CAATATCATC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.29, C:0.16, G:0.02, T:0.53
Consensus pattern (21 bp):
TCATCTATATTATTAGCATTA
Found at i:12616 original size:149 final size:149
Alignment explanation
Indices: 12346--12797 Score: 746
Period size: 149 Copynumber: 3.0 Consensus size: 149
12336 CCGAAGTGCA
*
12346 CGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
12411 TATATACATATACTAAGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 TATATACATATACTAAGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
12476 TATATATCCCGAAGGACCT
131 TATATATCCCGAAGGACCT
*
12495 CGTAGAATTGCACTGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
12560 TATATACATATACTAAGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 TATATACATATACTAAGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
*
12625 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCT
12644 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
* * ** * * * * *
12709 CATATACATATACTAAGGACCAAGTATGTACCTCA-AAGACCTCATAAATGTTCCAAAGAATATA
66 TATATACATATACTAAGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
* * *
12773 CACATGTCCCGAAGGA-CT
131 TATATATCCCGAAGGACCT
12791 GCGTAGA
1 -CGTAGA
12798 CCCTCAACTC
Statistics
Matches: 285, Mismatches: 17, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
147 1 0.00
148 44 0.15
149 240 0.84
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
TATATACATATACTAAGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
TATATATCCCGAAGGACCT
Found at i:14298 original size:64 final size:63
Alignment explanation
Indices: 14145--14300 Score: 170
Period size: 64 Copynumber: 2.4 Consensus size: 63
14135 TAATGAAGGT
* * * * * *
14145 ATGCATCGATGCATTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACTCCA-TATGCATCGATACATAAATCCTATTCGATGTTTCTATTTAAT-GGA
* * *
14210 ATGCATCGATGCACTCCTTATGCATCGATACATAAATCCTATTCGATGTTTTCTTTTTAAAT-TA
1 ATGCATCGATGCACTCCATATGCATCGATACATAAATCCTATTCGATG-TTTCTATTT-AATGGA
* *
14274 ATGCATCGATGCACTGCATGTGCATCG
1 ATGCATCGATGCACTCCATATGCATCG
14301 GTGCACCTTA
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
64 52 0.68
65 22 0.29
66 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (63 bp):
ATGCATCGATGCACTCCATATGCATCGATACATAAATCCTATTCGATGTTTCTATTTAATGGA
Found at i:17243 original size:21 final size:21
Alignment explanation
Indices: 17219--17273 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
17209 ACATATATCG
* *
17219 TCATCTATTTTCTTAGCATTA
1 TCATCTATATTATTAGCATTA
* *
17240 TCATATATATTATTATCATTA
1 TCATCTATATTATTAGCATTA
17261 TC-TCTATCATTAT
1 TCATCTAT-ATTAT
17274 CATCAAATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 4 0.14
21 24 0.86
ACGTcount: A:0.29, C:0.16, G:0.02, T:0.53
Consensus pattern (21 bp):
TCATCTATATTATTAGCATTA
Found at i:17278 original size:21 final size:21
Alignment explanation
Indices: 17235--17278 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
17225 ATTTTCTTAG
*
17235 CATTATCATATATATTATTAT
1 CATTATCATATATATTATCAT
*
17256 CATTATC-TCTATCATTATCAT
1 CATTATCATATAT-ATTATCAT
17277 CA
1 CA
17279 AATTATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.34, C:0.18, G:0.00, T:0.48
Consensus pattern (21 bp):
CATTATCATATATATTATCAT
Found at i:17763 original size:149 final size:149
Alignment explanation
Indices: 17491--17942 Score: 762
Period size: 149 Copynumber: 3.0 Consensus size: 149
17481 CCGAAGTGCA
17491 CGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1 CGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
*
17556 TATATACATATACTAAGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTGCACAGAATATA
66 TATATACATATACTAAGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
17621 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
*
17640 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1 CGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
17705 TATATACATATACTAAGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 TATATACATATACTAAGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
*
17770 TATATATCCCGAAAGACCG
131 TATATATCCCGAAGGACCG
*
17789 CGTAGAATTTCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1 CGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
* * * * * * * * *
17854 CATATACATATACTAAGGACCAGGTATGTGCCTCA-AAGACCTCATAAATGTTCCAAAGAATATA
66 TATATACATATACTAAGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
* *
17918 CATATGTCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
17937 CGTAGA
1 CGTAGA
17943 CCCTCGACTC
Statistics
Matches: 287, Mismatches: 16, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
148 47 0.16
149 240 0.84
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (149 bp):
CGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
TATATACATATACTAAGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
TATATATCCCGAAGGACCG
Found at i:19424 original size:64 final size:63
Alignment explanation
Indices: 19291--19451 Score: 180
Period size: 64 Copynumber: 2.5 Consensus size: 63
19281 TAATAAAGGT
* * * * *
19291 ATGCATCGATGCATTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACTCCA-TATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGA
* * * *
19356 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATTCTATTCGATGTTTTCTTTTTAAAT-TA
1 ATGCATCGATGCACTCCATATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGGA
* *
19420 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACTCCATATGCATCGATGCA
19452 CCTTAAACAA
Statistics
Matches: 82, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 57 0.70
65 22 0.27
66 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (63 bp):
ATGCATCGATGCACTCCATATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGA
Found at i:32701 original size:29 final size:29
Alignment explanation
Indices: 32669--32741 Score: 146
Period size: 29 Copynumber: 2.5 Consensus size: 29
32659 AAAGTAAACT
32669 AAAATAAAATGACCAGATAAAGAAAGCAC
1 AAAATAAAATGACCAGATAAAGAAAGCAC
32698 AAAATAAAATGACCAGATAAAGAAAGCAC
1 AAAATAAAATGACCAGATAAAGAAAGCAC
32727 AAAATAAAATGACCA
1 AAAATAAAATGACCA
32742 CAAAATATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.63, C:0.14, G:0.12, T:0.11
Consensus pattern (29 bp):
AAAATAAAATGACCAGATAAAGAAAGCAC
Found at i:32743 original size:16 final size:16
Alignment explanation
Indices: 32695--32748 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
32685 ATAAAGAAAG
32695 CACAAAATAAAATGAC
1 CACAAAATAAAATGAC
* *
32711 CAGATAAA-GAAA-G--
1 CACA-AAATAAAATGAC
32724 CACAAAATAAAATGAC
1 CACAAAATAAAATGAC
32740 CACAAAATA
1 CACAAAATA
32749 TATACAAAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 10
0.67 0.09 0.23
Matches are distributed among these distances:
12 3 0.10
13 6 0.21
14 1 0.03
15 1 0.03
16 15 0.52
17 3 0.10
ACGTcount: A:0.63, C:0.17, G:0.09, T:0.11
Consensus pattern (16 bp):
CACAAAATAAAATGAC
Found at i:39660 original size:32 final size:32
Alignment explanation
Indices: 39624--39686 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
39614 TATGTTTTTT
39624 ATTATCTGAAAGCAATATAAATTCTATTGTGC
1 ATTATCTGAAAGCAATATAAATTCTATTGTGC
* * *
39656 ATTATCTGAATGCAATATTAATTCTGTTGTG
1 ATTATCTGAAAGCAATATAAATTCTATTGTG
39687 ACTCATACAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.41
Consensus pattern (32 bp):
ATTATCTGAAAGCAATATAAATTCTATTGTGC
Found at i:42091 original size:8 final size:8
Alignment explanation
Indices: 42078--42116 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
42068 TTAGCTAAAC
42078 TTAAAAAT
1 TTAAAAAT
42086 TT-AAAAT
1 TTAAAAAT
42093 TTAAAAAT
1 TTAAAAAT
*
42101 TAAAAAAAT
1 T-TAAAAAT
42110 TTAAAAA
1 TTAAAAA
42117 AATAATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 7 0.26
8 13 0.48
9 7 0.26
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
TTAAAAAT
Found at i:42215 original size:3 final size:3
Alignment explanation
Indices: 42201--42240 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
42191 AAAGAAAATG
* * *
42201 ATA ATA ACA ATA ATA ATA ATA TTA ATA CTA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
42241 AACAGAATGT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:44223 original size:85 final size:85
Alignment explanation
Indices: 44080--45085 Score: 1308
Period size: 85 Copynumber: 11.8 Consensus size: 85
44070 CACTATCATC
* *
44080 GAGCTGAATGGAATCGAACTCAAAGGTTTTTGTTGACAGATAG--CTTCTCTAGACTTAAGCTAT
1 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTC--GACTTGAGCTAT
* *
44143 GCTGTAAATTTGATATGTCATT
64 GCTGTAAATTTGATATGCCCTT
* * *
44165 GAGCTGAATGGAATCGAACTCAAAGGTTTTTGTTGACAGATAG-CTTCTCTCGACTTAAGCTATG
1 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCT-TCTCGACTTGAGCTATG
*
44229 CTGTAAATTTGATATGCCATT
65 CTGTAAATTTGATATGCCCTT
* * *
44250 GAGCTGAATGGAATTGAACTCGAAGGTTTTTGTTGATAGATAACCCTTCTC-ACCTTGAGCTATG
1 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGA-CTTGAGCTATG
44314 CTGTAAATTTGATATGCCCTT
65 CTGTAAATTTGATATGCCCTT
* * * * *
44335 GAGCTGAATGGAATCGAACTCAAAGGTTTTTGTTGATAGATAGCCTTTCTTGCCTTGAGCTATGC
1 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGACTTGAGCTATGC
*
44400 TGTAAATTTTATATGCCCTT
66 TGTAAATTTGATATGCCCTT
* * * *
44420 GAGCTGAATGTAATCAAACTCGAAGGTTTTTGTTGGCAGATAACCCTTCTC-ACCTTGAGCTATG
1 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGA-CTTGAGCTATG
44484 CTGTAAATTTGATATGCCCTT
65 CTGTAAATTTGATATGCCCTT
* * * *
44505 GAGCTGAATGGAATCAAACTC-ACTGGTTTTTGTTGACAGATAGCCCTTTTCGTCTTGAGCTATG
1 GAGCTGAATGGAATCGAACTCGA-AGGTTTTTGTTGACAGATAGCCCTTCTCGACTTGAGCTATG
44569 CTGTAAATTTGATATGCCCTT
65 CTGTAAATTTGATATGCCCTT
* * * * * * *
44590 GAGGTGAATGGAATCAAACTCGAAGGTTTTTTGTTGACAAATATCCCTTTTTGCCTTGAGCTATG
1 GAGCTGAATGGAATCGAACTCGAAGG-TTTTTGTTGACAGATAGCCCTTCTCGACTTGAGCTATG
*
44655 TTGTAAATTTGATATGCCCTT
65 CTGTAAATTTGATATGCCCTT
* * *
44676 GAGCTGAATGTAAGCGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTC-ACCTTGAGCTATG
1 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGA-CTTGAGCTATG
44740 CTGTAAATTTGATATGCCCTT
65 CTGTAAATTTGATATGCCCTT
* * * * * * *
44761 GACCTGAATGTAATTGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTTTGT
1 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGACTTGAGCTATGC
*
44826 TGTAAATTTGATATGCGCTT
66 TGTAAATTTGATATGCCCTT
* * *
44846 GAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGATATGC
1 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGACTTGAGCTATGC
*
44911 TGTAAATTTGATATGCCATT
66 TGTAAATTTGATATGCCCTT
* * * * * * *
44931 TAGCTTAATGTAATCGAACTCGAAGGTTTTTGTTAACAGATATCCCTTCTC-ACCTTAAGCTATA
1 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGA-CTTGAGCTATG
*
44995 CTGTAAATTTTATATGCCCTT
65 CTGTAAATTTGATATGCCCTT
* * * * * * *
45016 GAGTTGAATGTAATCGAACTCGAATGTTTTTGTTGACAGATAGCTCTTCTCGTCTTGAGCCATTC
1 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGACTTGAGCTATGC
45081 TGTAA
66 TGTAA
45086 TAGGCTGGGA
Statistics
Matches: 822, Mismatches: 85, Indels: 28
0.88 0.09 0.03
Matches are distributed among these distances:
84 2 0.00
85 736 0.90
86 80 0.10
87 4 0.00
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (85 bp):
GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGACTTGAGCTATGC
TGTAAATTTGATATGCCCTT
Found at i:49036 original size:17 final size:15
Alignment explanation
Indices: 49016--49071 Score: 58
Period size: 17 Copynumber: 3.5 Consensus size: 15
49006 GGAGTGCAAA
49016 AAAAAGAAAGAAAAGAC
1 AAAAAG-AAGAAAA-AC
*
49033 AAAAAGAAGAAAATTC
1 AAAAAGAAGAAAA-AC
*
49049 AGAAAAGAAGAAAAAG
1 A-AAAAGAAGAAAAAC
49065 AAAAAGA
1 AAAAAGA
49072 TTTCAAAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
15 6 0.18
16 10 0.29
17 18 0.53
ACGTcount: A:0.75, C:0.04, G:0.18, T:0.04
Consensus pattern (15 bp):
AAAAAGAAGAAAAAC
Found at i:49062 original size:26 final size:26
Alignment explanation
Indices: 49024--49087 Score: 80
Period size: 25 Copynumber: 2.5 Consensus size: 26
49014 AAAAAAAGAA
*
49024 AGAAAAGACAAAAAGAAGAAA-A-TTC
1 AGAAAAGAGAAAAAGAA-AAAGATTTC
49049 AGAAAAGAAGAAAAAGAAAAAGATTTC
1 AGAAAAG-AGAAAAAGAAAAAGATTTC
49076 A-AAAAGAGAAAA
1 AGAAAAGAGAAAA
49088 GCAAGCCAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
25 16 0.46
26 15 0.43
27 4 0.11
ACGTcount: A:0.70, C:0.05, G:0.17, T:0.08
Consensus pattern (26 bp):
AGAAAAGAGAAAAAGAAAAAGATTTC
Found at i:56441 original size:8 final size:8
Alignment explanation
Indices: 56428--56469 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
56418 TCGAATTATG
56428 AAAAGAAA
1 AAAAGAAA
56436 AAAAG-AA
1 AAAAGAAA
56443 AAAAGAAA
1 AAAAGAAA
* *
56451 TAAATAAA
1 AAAAGAAA
56459 TAAAAGAAA
1 -AAAAGAAA
56468 AA
1 AA
56470 GAAAAAGATA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 7 0.25
8 15 0.54
9 6 0.21
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (8 bp):
AAAAGAAA
Found at i:56704 original size:24 final size:24
Alignment explanation
Indices: 56677--56738 Score: 115
Period size: 24 Copynumber: 2.6 Consensus size: 24
56667 CTCGAAAAAG
56677 AATTTGCAAATAACGGAGGTACCC
1 AATTTGCAAATAACGGAGGTACCC
56701 AATTTGCAAATAACGGAGGTACCC
1 AATTTGCAAATAACGGAGGTACCC
*
56725 AATTTGCAATTAAC
1 AATTTGCAAATAAC
56739 CCCTCCCTCG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (24 bp):
AATTTGCAAATAACGGAGGTACCC
Found at i:74621 original size:38 final size:38
Alignment explanation
Indices: 74570--74651 Score: 164
Period size: 38 Copynumber: 2.2 Consensus size: 38
74560 GGATGTAAAA
74570 TCAGGTAATCATTCAAGTTTCATTCGGATCCTGTCAGG
1 TCAGGTAATCATTCAAGTTTCATTCGGATCCTGTCAGG
74608 TCAGGTAATCATTCAAGTTTCATTCGGATCCTGTCAGG
1 TCAGGTAATCATTCAAGTTTCATTCGGATCCTGTCAGG
74646 TCAGGT
1 TCAGGT
74652 CAAATCAGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (38 bp):
TCAGGTAATCATTCAAGTTTCATTCGGATCCTGTCAGG
Found at i:75050 original size:2 final size:2
Alignment explanation
Indices: 75043--75090 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
75033 TATGGTCATT
75043 TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
75084 TA TA TA T
1 TA TA TA T
75091 TTTAAGAATT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:75832 original size:12 final size:13
Alignment explanation
Indices: 75817--75848 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
75807 TATATATAAC
75817 ATAATATG-TATG
1 ATAATATGTTATG
75829 ATAA-ATGTTATG
1 ATAATATGTTATG
75841 ATAATATG
1 ATAATATG
75849 ATGCATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.17
12 12 0.67
13 3 0.17
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.41
Consensus pattern (13 bp):
ATAATATGTTATG
Found at i:75981 original size:18 final size:18
Alignment explanation
Indices: 75948--75997 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
75938 CTTATAACAC
75948 ATATAA-TATA-AGTATAT
1 ATATAAGTATATA-TATAT
* *
75965 GTATTAGTATATATATAT
1 ATATAAGTATATATATAT
75983 ATATAAGTATATATA
1 ATATAAGTATATATA
75998 CATAAGTGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 4 0.15
18 22 0.81
19 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (18 bp):
ATATAAGTATATATATAT
Found at i:76023 original size:12 final size:12
Alignment explanation
Indices: 76006--76032 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
75996 TACATAAGTG
76006 TATGTATGTATA
1 TATGTATGTATA
76018 TATGTATGTATA
1 TATGTATGTATA
76030 TAT
1 TAT
76033 CATTAAACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (12 bp):
TATGTATGTATA
Found at i:76568 original size:26 final size:23
Alignment explanation
Indices: 76533--76597 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 23
76523 ATTTTAAAGT
*
76533 TTTAAGTTAAATTATATTTAAACTAA
1 TTTAAATTAAATTATA-TTAAA-T-A
*
76559 TTTAAATTAAACT-TA-TAAATA
1 TTTAAATTAAATTATATTAAATA
76580 TTTAAATTAAATTTATAT
1 TTTAAATTAAA-TTATAT
76598 AATTAATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
21 12 0.36
22 2 0.06
23 6 0.18
25 2 0.06
26 11 0.33
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (23 bp):
TTTAAATTAAATTATATTAAATA
Found at i:76595 original size:21 final size:22
Alignment explanation
Indices: 76539--76596 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
76529 AAGTTTTAAG
* *
76539 TTAAATTATATTTA-AACTAAT
1 TTAAATTAAATTTATAAATAAT
*
76560 TTAAATTAAACTTATAAAT-AT
1 TTAAATTAAATTTATAAATAAT
76581 TTAAATTAAATTTATA
1 TTAAATTAAATTTATA
76597 TAATTAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 29 0.91
22 3 0.09
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (22 bp):
TTAAATTAAATTTATAAATAAT
Found at i:76658 original size:14 final size:14
Alignment explanation
Indices: 76641--76686 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
76631 TTAATTAAAT
**
76641 TAATTTAATTATTA
1 TAATTTAAAAATTA
76655 TAA-TTAAAAATTA
1 TAATTTAAAAATTA
*
76668 TAATATAAAAATTA
1 TAATTTAAAAATTA
76682 TAATT
1 TAATT
76687 AATATAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
TAATTTAAAAATTA
Found at i:76661 original size:13 final size:13
Alignment explanation
Indices: 76645--76690 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
76635 TTAAATTAAT
*
76645 TTAATTATTATAA
1 TTAATAATTATAA
*
76658 TTAAAAATTATAA
1 TTAATAATTATAA
*
76671 TATAAAAATTATAA
1 T-TAATAATTATAA
76685 TTAATA
1 TTAATA
76691 TAAAAAGTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 16 0.55
14 13 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TTAATAATTATAA
Found at i:76668 original size:16 final size:16
Alignment explanation
Indices: 76647--76696 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 16
76637 AAATTAATTT
*
76647 AATTATTATAATTAAA
1 AATTATAATAATTAAA
76663 AATTATAAT-A-TAAA
1 AATTATAATAATTAAA
76677 AATTATAATTAATATAAA
1 AATTATAA-TAAT-TAAA
76695 AA
1 AA
76697 GTAAATTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
14 12 0.41
15 2 0.07
16 9 0.31
18 6 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AATTATAATAATTAAA
Found at i:80109 original size:193 final size:193
Alignment explanation
Indices: 79780--80165 Score: 747
Period size: 193 Copynumber: 2.0 Consensus size: 193
79770 TGGAGACATC
79780 AATCATGTGCTTGTCTAAGTCTCAACCGTCATCCATAGTTAAATTTTCGGTACACCTCCTGTAAC
1 AATCATGTGCTTGTCTAAGTCTCAACCGTCATCCATAGTTAAATTTTCGGTACACCTCCTGTAAC
*
79845 TCATTTGTTCCGTGTTTCATTCAGGGATGATCGAGAGGTTGATAGGGATGATTGTCTTCTTAAAA
66 TCATTTGTTCCGTGTTTCAATCAGGGATGATCGAGAGGTTGATAGGGATGATTGTCTTCTTAAAA
79910 AAATTAAATTCACATGTAATTTATTTTTTTACG-TTTTTTATCGATAATCTATTTTCATCTTCT
131 AAATTAAATTCACATGTAATTTATTTTTTTACGTTTTTTTATCGATAATCTATTTT-ATCTTCT
79973 AATCATGTGCTTGTCTAAGTCTCAACCGTCATCCATAGTTAAATTTTCGGTACACCTCCTGTAAC
1 AATCATGTGCTTGTCTAAGTCTCAACCGTCATCCATAGTTAAATTTTCGGTACACCTCCTGTAAC
80038 TCATTTGTTCCGTGTTTCAATCAGGGATGATCGAGAGGTTGATAGGGATGATTGTCTTCTTAAAA
66 TCATTTGTTCCGTGTTTCAATCAGGGATGATCGAGAGGTTGATAGGGATGATTGTCTTCTTAAAA
80103 AAATTAAATTCACATGTAATTTATTTTTTTACGTTTTTTTATCGATAATCTATTTTATCTTCT
131 AAATTAAATTCACATGTAATTTATTTTTTTACGTTTTTTTATCGATAATCTATTTTATCTTCT
80166 TAAAATTACA
Statistics
Matches: 191, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
193 169 0.88
194 22 0.12
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (193 bp):
AATCATGTGCTTGTCTAAGTCTCAACCGTCATCCATAGTTAAATTTTCGGTACACCTCCTGTAAC
TCATTTGTTCCGTGTTTCAATCAGGGATGATCGAGAGGTTGATAGGGATGATTGTCTTCTTAAAA
AAATTAAATTCACATGTAATTTATTTTTTTACGTTTTTTTATCGATAATCTATTTTATCTTCT
Found at i:91269 original size:22 final size:23
Alignment explanation
Indices: 91237--91285 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
91227 TTACATTCTG
* *
91237 CAAATATTTACTTAACTAACACC
1 CAAATATTTACATAAATAACACC
*
91260 CAAAT-TTTACATAAATAGCACC
1 CAAATATTTACATAAATAACACC
91282 CAAA
1 CAAA
91286 CAGAATTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.47, C:0.24, G:0.02, T:0.27
Consensus pattern (23 bp):
CAAATATTTACATAAATAACACC
Found at i:92449 original size:40 final size:40
Alignment explanation
Indices: 92389--92464 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
92379 ACATGGTGAC
*
92389 ACGTTGGGTAAGGCGCGGTGCATGGGCCGCACCTTCTGCT
1 ACGTAGGGTAAGGCGCGGTGCATGGGCCGCACCTTCTGCT
* * *
92429 ACGTAGGGTATGGCGCGGTGCATGGGTCGCGCCTTC
1 ACGTAGGGTAAGGCGCGGTGCATGGGCCGCACCTTC
92465 CTTATAGTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.12, C:0.26, G:0.39, T:0.22
Consensus pattern (40 bp):
ACGTAGGGTAAGGCGCGGTGCATGGGCCGCACCTTCTGCT
Found at i:92737 original size:16 final size:13
Alignment explanation
Indices: 92707--92732 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
92697 TTGTAAGGTA
92707 ATTTTTTTATAAT
1 ATTTTTTTATAAT
92720 ATTTTTTTATAAT
1 ATTTTTTTATAAT
92733 TATATATGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTTTTTTATAAT
Found at i:93619 original size:91 final size:91
Alignment explanation
Indices: 93512--93700 Score: 378
Period size: 91 Copynumber: 2.1 Consensus size: 91
93502 TGGGTTCACG
93512 AACAATCCATATGGCAACATCGCGTCCAGTTCAAGGGGAAGAAATTCATCTGCCAATTTCTTTGA
1 AACAATCCATATGGCAACATCGCGTCCAGTTCAAGGGGAAGAAATTCATCTGCCAATTTCTTTGA
93577 CCTTAATATGGAGATGCCCTCGATGC
66 CCTTAATATGGAGATGCCCTCGATGC
93603 AACAATCCATATGGCAACATCGCGTCCAGTTCAAGGGGAAGAAATTCATCTGCCAATTTCTTTGA
1 AACAATCCATATGGCAACATCGCGTCCAGTTCAAGGGGAAGAAATTCATCTGCCAATTTCTTTGA
93668 CCTTAATATGGAGATGCCCTCGATGC
66 CCTTAATATGGAGATGCCCTCGATGC
93694 AACAATC
1 AACAATC
93701 TGTGCAGTTT
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 98 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (91 bp):
AACAATCCATATGGCAACATCGCGTCCAGTTCAAGGGGAAGAAATTCATCTGCCAATTTCTTTGA
CCTTAATATGGAGATGCCCTCGATGC
Found at i:96139 original size:17 final size:17
Alignment explanation
Indices: 96117--96154 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
96107 TCAGATATAC
96117 CTGCGGGGTGTACGTCG
1 CTGCGGGGTGTACGTCG
96134 CTGCGGGGTGTACGTCG
1 CTGCGGGGTGTACGTCG
96151 CTGC
1 CTGC
96155 AGACGGTGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.05, C:0.26, G:0.45, T:0.24
Consensus pattern (17 bp):
CTGCGGGGTGTACGTCG
Found at i:97810 original size:17 final size:17
Alignment explanation
Indices: 97788--97824 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
97778 CAAAAAAAAT
97788 TAATTAAAA-ATATTAAA
1 TAATTAAAATA-ATTAAA
97805 TAATTAAAATAATTAAA
1 TAATTAAAATAATTAAA
97822 TAA
1 TAA
97825 AATACTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 18 0.95
18 1 0.05
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TAATTAAAATAATTAAA
Found at i:97839 original size:11 final size:12
Alignment explanation
Indices: 97803--97852 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
97793 AAAAATATTA
*
97803 AATAATTAAAAT
1 AATAAATAAAAT
97815 AATTAAATAAAAT
1 AA-TAAATAAAAT
*
97828 ACTAAA-AAAAT
1 AATAAATAAAAT
*
97839 AATAAATATAAT
1 AATAAATAAAAT
97851 AA
1 AA
97853 AATATACCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 10 0.31
12 12 0.38
13 10 0.31
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (12 bp):
AATAAATAAAAT
Found at i:97895 original size:20 final size:20
Alignment explanation
Indices: 97872--97914 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
97862 TAAAGAGCTA
* *
97872 TGAGAGAATTTAAGAGTATT
1 TGAGAGAAGTTAAGAGGATT
*
97892 TGAGAGAAGTTGAGAGGATT
1 TGAGAGAAGTTAAGAGGATT
97912 TGA
1 TGA
97915 TGTGATGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.33, T:0.30
Consensus pattern (20 bp):
TGAGAGAAGTTAAGAGGATT
Found at i:97904 original size:10 final size:10
Alignment explanation
Indices: 97872--97914 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
97862 TAAAGAGCTA
97872 TGAGAGAATT
1 TGAGAGAATT
* *
97882 TAAGAGTATT
1 TGAGAGAATT
*
97892 TGAGAGAAGT
1 TGAGAGAATT
*
97902 TGAGAGGATT
1 TGAGAGAATT
97912 TGA
1 TGA
97915 TGTGATGAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.37, C:0.00, G:0.33, T:0.30
Consensus pattern (10 bp):
TGAGAGAATT
Found at i:101770 original size:20 final size:20
Alignment explanation
Indices: 101736--101786 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
101726 AAAAGTGTTG
* *
101736 TACTATATG-ATAGTATTGA
1 TACTGTATGAATAGTATCGA
*
101755 TATTGTATGAATAGTATCGA
1 TACTGTATGAATAGTATCGA
101775 TACTGTAATGAA
1 TACTGT-ATGAA
101787 CAATGTCGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 7 0.27
20 14 0.54
21 5 0.19
ACGTcount: A:0.37, C:0.06, G:0.18, T:0.39
Consensus pattern (20 bp):
TACTGTATGAATAGTATCGA
Found at i:101843 original size:20 final size:20
Alignment explanation
Indices: 101814--101861 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
101804 AATTCCAAAA
* *
101814 TGCTATAGGGGTATCGATAC
1 TGCTACAGGGGTACCGATAC
101834 TGCTACAGGGGTACCGATAC
1 TGCTACAGGGGTACCGATAC
101854 TGCTACAG
1 TGCTACAG
101862 TAATTTAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (20 bp):
TGCTACAGGGGTACCGATAC
Found at i:105318 original size:19 final size:20
Alignment explanation
Indices: 105294--105339 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
105284 AATTCCAGAA
* *
105294 TGCTACA-GGGTATCGATAC
1 TGCTACAGGGGTACCAATAC
105313 TGCTACAGGGGTACCAATAC
1 TGCTACAGGGGTACCAATAC
105333 TGCTACA
1 TGCTACA
105340 ATAATTTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (20 bp):
TGCTACAGGGGTACCAATAC
Found at i:105743 original size:34 final size:34
Alignment explanation
Indices: 105680--105744 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
105670 CCTTTTGTAA
*
105680 AGGGGAAAGGTTCTAGTTGATCCCGTGAAAAGCT
1 AGGGGAAAGGTTCTAGTTGATCCCATGAAAAGCT
*
105714 AGGGGAAAGGTTCTAGTTTAGT-CCATGAAAA
1 AGGGGAAAGGTTCTAGTTGA-TCCCATGAAAA
105745 AATAGGGAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 27 0.96
35 1 0.04
ACGTcount: A:0.32, C:0.12, G:0.31, T:0.25
Consensus pattern (34 bp):
AGGGGAAAGGTTCTAGTTGATCCCATGAAAAGCT
Found at i:108114 original size:20 final size:20
Alignment explanation
Indices: 108065--108114 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
108055 ACAGTTTCCA
108065 AATTCGCAACGCGAATATGT
1 AATTCGCAACGCGAATATGT
* *
108085 AAATCGCAACGCGAATTTGT
1 AATTCGCAACGCGAATATGT
*
108105 AATTCACAAC
1 AATTCGCAAC
108115 ACATAAGTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (20 bp):
AATTCGCAACGCGAATATGT
Found at i:108132 original size:40 final size:40
Alignment explanation
Indices: 108081--108195 Score: 121
Period size: 41 Copynumber: 2.9 Consensus size: 40
108071 CAACGCGAAT
*
108081 ATGT-AAA-TCGCAACGCGAATTTGTAATTCACAACACAT-A
1 ATGTCAAATTCGCAACGCG-ATTTCTAATTCACAACAC-TGA
* *
108120 A-GTCAAATTCGCAACGCGATTTCCAAATTCGCAACACTGA
1 ATGTCAAATTCGCAACGCGATTT-CTAATTCACAACACTGA
* *
108160 ATTTCAAATTCGCAACTCGATTTCTGAATTCACAAC
1 ATGTCAAATTCGCAACGCGATTTCT-AATTCACAAC
108196 TCGATTTTCG
Statistics
Matches: 63, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
38 2 0.03
39 9 0.14
40 24 0.38
41 28 0.44
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (40 bp):
ATGTCAAATTCGCAACGCGATTTCTAATTCACAACACTGA
Found at i:108146 original size:20 final size:20
Alignment explanation
Indices: 108123--108215 Score: 98
Period size: 20 Copynumber: 4.6 Consensus size: 20
108113 ACACATAAGT
*
108123 CAAATTCGCAACGCGATTTC
1 CAAATTCGCAACTCGATTTC
*
108143 CAAATTCGCAACACTGAATTT-
1 CAAATTCGCAACTC-G-ATTTC
108164 CAAATTCGCAACTCGATTTC
1 CAAATTCGCAACTCGATTTC
** * *
108184 TGAATTCACAACTCGATTTT
1 CAAATTCGCAACTCGATTTC
*
108204 CGAATTCGCAAC
1 CAAATTCGCAAC
108216 ACGGATTTTA
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
19 4 0.06
20 40 0.65
21 14 0.23
22 4 0.06
ACGTcount: A:0.32, C:0.27, G:0.12, T:0.29
Consensus pattern (20 bp):
CAAATTCGCAACTCGATTTC
Found at i:108181 original size:41 final size:40
Alignment explanation
Indices: 108059--108215 Score: 124
Period size: 40 Copynumber: 3.9 Consensus size: 40
108049 CACAACACAG
* *
108059 TTTCCAAATTCGCAACGCGAATATGT-AAA-TCGCAACGCGAA
1 TTTCCAAATTCACAACACGAAT-T-TCAAATTCGCAACGCG-A
** **
108100 TTT-GTAATTCACAACAC-ATAAGTCAAATTCGCAACGCGA
1 TTTCCAAATTCACAACACGA-ATTTCAAATTCGCAACGCGA
* *
108139 TTTCCAAATTCGCAACACTGAATTTCAAATTCGCAACTCGA
1 TTTCCAAATTCACAACAC-GAATTTCAAATTCGCAACGCGA
** * * *
108180 TTTCTGAATTCACAACTCGATTTTCGAATTCGCAAC
1 TTTCCAAATTCACAACACGAATTTCAAATTCGCAAC
108216 ACGGATTTTA
Statistics
Matches: 92, Mismatches: 18, Indels: 13
0.75 0.15 0.11
Matches are distributed among these distances:
38 1 0.01
39 8 0.09
40 48 0.52
41 34 0.37
42 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (40 bp):
TTTCCAAATTCACAACACGAATTTCAAATTCGCAACGCGA
Found at i:108223 original size:41 final size:41
Alignment explanation
Indices: 108105--108223 Score: 118
Period size: 41 Copynumber: 2.9 Consensus size: 41
108095 GCGAATTTGT
* *
108105 AATTCACAACACAT-AA-GTCAAATTCGCAACGCGATTTCCA
1 AATTCACAACAC-TGAATTTCAAATTCGCAACACGATTTCCA
* * **
108145 AATTCGCAACACTGAATTTCAAATTCGCAACTCGATTTCTG
1 AATTCACAACACTGAATTTCAAATTCGCAACACGATTTCCA
* * *
108186 AATTCACAACTC-GATTTTCGAATTCGCAACACGGATTT
1 AATTCACAACACTGAATTTCAAATTCGCAACAC-GATTT
108224 TAATTTCGCA
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
39 1 0.02
40 30 0.45
41 35 0.53
ACGTcount: A:0.34, C:0.25, G:0.12, T:0.29
Consensus pattern (41 bp):
AATTCACAACACTGAATTTCAAATTCGCAACACGATTTCCA
Found at i:108248 original size:18 final size:20
Alignment explanation
Indices: 108208--108255 Score: 73
Period size: 18 Copynumber: 2.5 Consensus size: 20
108198 GATTTTCGAA
108208 TTCGCAACACGGATTTTAAT
1 TTCGCAACACGGATTTTAAT
*
108228 TTCGCAACA-GG-TTTTATT
1 TTCGCAACACGGATTTTAAT
108246 TTCGCAACAC
1 TTCGCAACAC
108256 AAATGTTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 15 0.58
19 2 0.08
20 9 0.35
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (20 bp):
TTCGCAACACGGATTTTAAT
Found at i:108994 original size:12 final size:12
Alignment explanation
Indices: 108973--109006 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
108963 ACCACATTTC
*
108973 CAATACCAAACA
1 CAATATCAAACA
108985 CAATATCAAACA
1 CAATATCAAACA
*
108997 CAATCTCAAA
1 CAATATCAAA
109007 ACCCATAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:109183 original size:24 final size:24
Alignment explanation
Indices: 109132--109185 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
109122 GTATTCAAAA
*
109132 TTTGATATTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCAGAC
* * *
109156 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATATTGGTCAATACCCAGAC
109180 TTTGAT
1 TTTGAT
109186 GATGTTTCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCAGAC
Found at i:111800 original size:20 final size:20
Alignment explanation
Indices: 111775--111839 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
111765 GCGATTGTTT
111775 CGAAAGTAAAATTCGAAACG
1 CGAAAGTAAAATTCGAAACG
*
111795 CGAAAGTAAAATTCGCAACG
1 CGAAAGTAAAATTCGAAACG
* * *
111815 CGAAAATCAAATTCGTAACG
1 CGAAAGTAAAATTCGAAACG
*
111835 TGAAA
1 CGAAA
111840 ATCACAACAC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.48, C:0.17, G:0.18, T:0.17
Consensus pattern (20 bp):
CGAAAGTAAAATTCGAAACG
Found at i:111920 original size:20 final size:20
Alignment explanation
Indices: 111897--111961 Score: 103
Period size: 20 Copynumber: 3.2 Consensus size: 20
111887 CAATCGCAAC
* *
111897 GCGAATTTGACTTTCGCGTT
1 GCGAATTTGATTTTCGAGTT
111917 GCGAATTTGATTTTCGAGTT
1 GCGAATTTGATTTTCGAGTT
111937 GCGAATTTGATTTTCGAGTT
1 GCGAATTTGATTTTCGAGTT
*
111957 CCGAA
1 GCGAA
111962 AGTGTACCTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.20, C:0.15, G:0.25, T:0.40
Consensus pattern (20 bp):
GCGAATTTGATTTTCGAGTT
Found at i:113452 original size:21 final size:20
Alignment explanation
Indices: 113426--113496 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 20
113416 GTGAATTGGG
113426 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAACGGTGGGAGGG-C
* **
113447 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGA-GGGC
* *
113468 CTTTTGAACGGTGGG-GGGG
1 CTCTTGAACGGTGGGAGGGC
113487 CTCTTGAACG
1 CTCTTGAACG
113497 ATGACAGGTG
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
19 12 0.30
21 25 0.62
22 3 0.08
ACGTcount: A:0.18, C:0.20, G:0.39, T:0.23
Consensus pattern (20 bp):
CTCTTGAACGGTGGGAGGGC
Found at i:113663 original size:12 final size:12
Alignment explanation
Indices: 113644--113691 Score: 62
Period size: 12 Copynumber: 4.1 Consensus size: 12
113634 GGGTCGCTAA
113644 AAATAAATTAAT
1 AAATAAATTAAT
* *
113656 ACATAAATTAGT
1 AAATAAATTAAT
*
113668 AAATAAATAAAT
1 AAATAAATTAAT
113680 AAATAAA-TAAT
1 AAATAAATTAAT
113691 A
1 A
113692 CCGAAAAAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
11 4 0.13
12 26 0.87
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (12 bp):
AAATAAATTAAT
Found at i:113676 original size:4 final size:4
Alignment explanation
Indices: 113644--113689 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
113634 GGGTCGCTAA
* * * *
113644 AAAT AAAT TAAT ACAT AAAT TAGT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
113690 TACCGAAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (4 bp):
AAAT
Found at i:113931 original size:21 final size:21
Alignment explanation
Indices: 113907--113959 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
113897 TGCACCATTG
*
113907 TCATCACGTAAAGTACCGACC
1 TCATCACGTAAAGCACCGACC
* *
113928 TCATCACGCAAAGCACTGACC
1 TCATCACGTAAAGCACCGACC
113949 TCATCACGTAA
1 TCATCACGTAA
113960 CTCCCCTAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.34, C:0.34, G:0.13, T:0.19
Consensus pattern (21 bp):
TCATCACGTAAAGCACCGACC
Found at i:115484 original size:19 final size:19
Alignment explanation
Indices: 115433--115486 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
115423 AGTAGTTTCT
*
115433 GAAACTTAAATTCGCAACGC
1 GAAAC-TAAAATCGCAACGC
*
115453 GAAAATGAAAATCGCAACGC
1 GAAACT-AAAATCGCAACGC
115473 GAAACTAAAATCGC
1 GAAACTAAAATCGC
115487 GTTGCGATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.30
20 21 0.70
ACGTcount: A:0.46, C:0.22, G:0.17, T:0.15
Consensus pattern (19 bp):
GAAACTAAAATCGCAACGC
Found at i:115518 original size:20 final size:20
Alignment explanation
Indices: 115493--115549 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
115483 TCGCGTTGCG
115493 ATTTTCGTGTTGCGAATTTC
1 ATTTTCGTGTTGCGAATTTC
115513 ATTTTCGTGTTGCGAATTTC
1 ATTTTCGTGTTGCGAATTTC
*
115533 ATTTCCGTGTTGCGAAT
1 ATTTTCGTGTTGCGAAT
115550 ATAAGTTTCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.16, C:0.16, G:0.21, T:0.47
Consensus pattern (20 bp):
ATTTTCGTGTTGCGAATTTC
Found at i:115910 original size:22 final size:22
Alignment explanation
Indices: 115883--115941 Score: 100
Period size: 22 Copynumber: 2.7 Consensus size: 22
115873 AGATGGAGAT
115883 AGACGGATTTCGCCGGAGATGG
1 AGACGGATTTCGCCGGAGATGG
115905 AGACGGATTTCGCCGGAGATGG
1 AGACGGATTTCGCCGGAGATGG
* *
115927 GGACGGATGTCGCCG
1 AGACGGATTTCGCCG
115942 TAGAGAGTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.20, C:0.20, G:0.42, T:0.17
Consensus pattern (22 bp):
AGACGGATTTCGCCGGAGATGG
Found at i:116067 original size:19 final size:19
Alignment explanation
Indices: 116045--116086 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
116035 AATATTGTGT
116045 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAAT-AAA
**
116064 TTCGCGTTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
116083 TTCG
1 TTCG
116087 CTTTAACTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (19 bp):
TTCGAATTGCGAAAATAAA
Found at i:121307 original size:170 final size:171
Alignment explanation
Indices: 121023--121355 Score: 535
Period size: 170 Copynumber: 1.9 Consensus size: 171
121013 TCAAGAAAGA
121023 ATGAAAATGTTGATGATGCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAAAAATGTCGAT
1 ATGAAAATGTTGATGATGCTGATCCAACTCCTTCTGCGATGGATTTGAGC-AAAAAAATGTCGAT
* *
121088 TCATCTCATTCTGTGATGGAATCGAACGAGATTTAGGTGTTGATCTACCTCATTCTGTGATAGAA
65 CCATCTCATTCTGTGATGGAATCGAACGAGATGTAGGTGTTGATCTACCTCATTCTGTGATAGAA
***
121153 TCGACCTAAAAGTTGATGTTGATCCAACTCCTTCTACAATGG
130 TCGACCTAAAAGTTGACACTGATCCAACTCCTTCTACAATGG
*
121195 ATGAAAATGTTGATGATGCTGATCCAACTCCTTCTGCGATGGATTT-ATGC-AAAAAATGTTGAT
1 ATGAAAATGTTGATGATGCTGATCCAACTCCTTCTGCGATGGATTTGA-GCAAAAAAATGTCGAT
* * *
121258 CCATCTCCTTCTGTGATGGAATCGAACGAGATGTCGGTGTTGATCTACCTCCTTCTGTGATAGAA
65 CCATCTCATTCTGTGATGGAATCGAACGAGATGTAGGTGTTGATCTACCTCATTCTGTGATAGAA
**
121323 TCGAGTTAAAAGTTGACACTGATCCAACTCCTT
130 TCGACCTAAAAGTTGACACTGATCCAACTCCTT
121356 TTGCGATGGA
Statistics
Matches: 149, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
170 100 0.67
171 1 0.01
172 48 0.32
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (171 bp):
ATGAAAATGTTGATGATGCTGATCCAACTCCTTCTGCGATGGATTTGAGCAAAAAAATGTCGATC
CATCTCATTCTGTGATGGAATCGAACGAGATGTAGGTGTTGATCTACCTCATTCTGTGATAGAAT
CGACCTAAAAGTTGACACTGATCCAACTCCTTCTACAATGG
Found at i:121453 original size:132 final size:133
Alignment explanation
Indices: 121213--121602 Score: 472
Period size: 132 Copynumber: 3.0 Consensus size: 133
121203 GTTGATGATG
* * * * *
121213 CTGATCCAACTCCTTCTGCGATGGATTT-A-TG--CA-AAAAATGTTGATCCATCTCCTTCTGTG
1 CTGATCCAACTCCTTTTGCGATGGATTTGAGAGAAAATAAAAATGTCGATCCACCTCCTTCTGTG
* * * *
121273 ATGGAATCGAACGAGATGTCGGTGTTGATCTACCTCCTTCTGTGATAGAATCGAGTTAAAAGTTG
66 ATGGAATCGAACAAGATATCGGTGTTGATCTACCTCCTTCTGTAATAGAATCGAGCTAAAAGTTG
121338 ACA
131 ACA
121341 CTGATCCAACTCCTTTTGCGATGGATTTGAGAGAAAATAAAAATGTCGATCCACCTCCTT-TGTG
1 CTGATCCAACTCCTTTTGCGATGGATTTGAGAGAAAATAAAAATGTCGATCCACCTCCTTCTGTG
* * *
121405 ATGGAATTGAACAAGATATTGGTGTTGATCTACCTCCTTTTGTAATAGAATCGAGCTAAAAGTTG
66 ATGGAATCGAACAAGATATCGGTGTTGATCTACCTCCTTCTGTAATAGAATCGAGCTAAAAGTTG
*
121470 ACG
131 ACA
* * * * * **
121473 CTGATCAAACTCCTTTTGTGATGAATTTGAGCGAAAATAAAAA-GTCGATCCACCTCCTACCATG
1 CTGATCCAACTCCTTTTGCGATGGATTTGAGAGAAAATAAAAATGTCGATCCACCTCCTTCTGTG
* * * * * * *
121537 ATGGAATCGAACGAGATATCAGTGCTGGTCTACCTCTTTCTGTGATAGATTCGAGC-AAACAGTT
66 ATGGAATCGAACAAGATATCGGTGTTGATCTACCTCCTTCTGTAATAGAATCGAGCTAAA-AGTT
121601 GA
130 GA
121603 ACAATCTCTT
Statistics
Matches: 225, Mismatches: 30, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
128 27 0.12
129 1 0.00
130 1 0.00
131 18 0.08
132 158 0.70
133 20 0.09
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (133 bp):
CTGATCCAACTCCTTTTGCGATGGATTTGAGAGAAAATAAAAATGTCGATCCACCTCCTTCTGTG
ATGGAATCGAACAAGATATCGGTGTTGATCTACCTCCTTCTGTAATAGAATCGAGCTAAAAGTTG
ACA
Found at i:121530 original size:44 final size:44
Alignment explanation
Indices: 121343--121530 Score: 98
Period size: 44 Copynumber: 4.3 Consensus size: 44
121333 AGTTGACACT
* * * * *
121343 GATCCAACTCCTTTTGCGATGGATTTGAGAGAAAATAAAAATGTC
1 GATCCACCTCCTTTTGTGATAGAATTGAGCGAAAATAAAAA-GTC
* * * **** *
121388 GATCCACCTCC-TTTGTGATGGAATTGAAC-AAGATATTGGTGTT
1 GATCCACCTCCTTTTGTGATAGAATTGAGCGAAAATA-AAAAGTC
* * * * ** *
121431 GATCTACCTCCTTTTGTAATAGAATCGAGCTAAAAGT-TGACG-C
1 GATCCACCTCCTTTTGTGATAGAATTGAGCGAAAA-TAAAAAGTC
* *
121474 TGATCAAACTCCTTTTGTGAT-GAATTTGAGCGAAAATAAAAAGTC
1 -GATCCACCTCCTTTTGTGATAGAA-TTGAGCGAAAATAAAAAGTC
121519 GATCCACCTCCT
1 GATCCACCTCCT
121531 ACCATGATGG
Statistics
Matches: 105, Mismatches: 30, Indels: 17
0.69 0.20 0.11
Matches are distributed among these distances:
43 21 0.20
44 69 0.66
45 14 0.13
46 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (44 bp):
GATCCACCTCCTTTTGTGATAGAATTGAGCGAAAATAAAAAGTC
Found at i:122253 original size:20 final size:20
Alignment explanation
Indices: 122228--122292 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
122218 GCCTGAGGGT
122228 CTTATGGCTGGCCCGAAGGA
1 CTTATGGCTGGCCCGAAGGA
* * * *
122248 CTTATGATCTTGCTCGAAAGA
1 CTTATG-GCTGGCCCGAAGGA
* *
122269 CTTATAGATGGCCCGAAGGA
1 CTTATGGCTGGCCCGAAGGA
122289 CTTA
1 CTTA
122293 CGCATCATGC
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 19 0.56
21 15 0.44
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (20 bp):
CTTATGGCTGGCCCGAAGGA
Found at i:122321 original size:42 final size:42
Alignment explanation
Indices: 122236--122341 Score: 133
Period size: 42 Copynumber: 2.5 Consensus size: 42
122226 GTCTTATGGC
* * *
122236 TGGCCCGAAGGACTTATG-ATCTTGCTCGAAAGACTTATAGA
1 TGGCCCGAAGGACTTACGCATCATGCTCGAAAGACTTACAGA
* * *
122277 TGGCCCGAAGGACTTACGCATCATGCTCGACATACTTACCGA
1 TGGCCCGAAGGACTTACGCATCATGCTCGAAAGACTTACAGA
* *
122319 TGGCCCGAAGTACTTACTCATCA
1 TGGCCCGAAGGACTTACGCATCA
122342 AGAAACCATT
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 17 0.30
42 39 0.70
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (42 bp):
TGGCCCGAAGGACTTACGCATCATGCTCGAAAGACTTACAGA
Found at i:122684 original size:42 final size:42
Alignment explanation
Indices: 122638--122843 Score: 256
Period size: 42 Copynumber: 4.9 Consensus size: 42
122628 AGTTTCTTAG
* *
122638 TTGTCATCAAGGAACCCCTATATGTCACGTTGGTCCCTCTAA
1 TTGTCATCAAGGAACCCCTACATATCACGTTGGTCCCTCTAA
122680 TTGTCATCAA-GAACCCCCTACATATCACGTTGGTCCCTC-AA
1 TTGTCATCAAGGAA-CCCCTACATATCACGTTGGTCCCTCTAA
* * *
122721 GCTTATCATTAAGGAACCCCTACATATCACGTTAGTCCCTCTAA
1 --TTGTCATCAAGGAACCCCTACATATCACGTTGGTCCCTCTAA
* *
122765 TTGTCATCAAGGAACCCCTACATATCACGTCT-GTCACTCAAGA
1 TTGTCATCAAGGAACCCCTACATATCACGT-TGGTCCCTCTA-A
* * *
122808 TTATCATCAAGGAACCCCTAAATATTACGTTGGTCC
1 TTGTCATCAAGGAACCCCTACATATCACGTTGGTCC
122844 ATCAAGCTTG
Statistics
Matches: 143, Mismatches: 13, Indels: 15
0.84 0.08 0.09
Matches are distributed among these distances:
41 5 0.03
42 69 0.48
43 64 0.45
44 5 0.03
ACGTcount: A:0.28, C:0.30, G:0.14, T:0.29
Consensus pattern (42 bp):
TTGTCATCAAGGAACCCCTACATATCACGTTGGTCCCTCTAA
Found at i:122751 original size:43 final size:42
Alignment explanation
Indices: 122636--122857 Score: 263
Period size: 43 Copynumber: 5.2 Consensus size: 42
122626 TTAGTTTCTT
* *
122636 AGTTGTCATCAAGGAACCCCTATATGTCACGTTGGTCCCTCTA
1 AGTTGTCATCAAGGAACCCCTACATATCACGTTGGTCCCTC-A
122679 A-TTGTCATCAA-GAACCCCCTACATATCACGTTGGTCCCTCA
1 AGTTGTCATCAAGGAA-CCCCTACATATCACGTTGGTCCCTCA
* * *
122720 AGCTTATCATTAAGGAACCCCTACATATCACGTTAGTCCCTCTA
1 AG-TTGTCATCAAGGAACCCCTACATATCACGTTGGTCCCTC-A
*
122764 A-TTGTCATCAAGGAACCCCTACATATCACGTCT-GTCACTCA
1 AGTTGTCATCAAGGAACCCCTACATATCACGT-TGGTCCCTCA
* * * *
122805 AGATTATCATCAAGGAACCCCTAAATATTACGTTGGTCCATCA
1 AG-TTGTCATCAAGGAACCCCTACATATCACGTTGGTCCCTCA
122848 AGCTTGTCAT
1 AG-TTGTCAT
122858 TAGCATGGTC
Statistics
Matches: 155, Mismatches: 15, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
41 7 0.05
42 68 0.44
43 75 0.48
44 5 0.03
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (42 bp):
AGTTGTCATCAAGGAACCCCTACATATCACGTTGGTCCCTCA
Found at i:122759 original size:85 final size:85
Alignment explanation
Indices: 122641--122843 Score: 302
Period size: 85 Copynumber: 2.4 Consensus size: 85
122631 TTCTTAGTTG
* *
122641 TCATCAAGGAACCCCTATATGTCACGTTGGTCCCTCTAATTGTCATCAA-GAACCCCCTACATAT
1 TCATCAAGGAACCCCTAAATATCACGTTGGTCCCTCTAATTGTCATCAAGGAA-CCCCTACATAT
* *
122705 CACGT-TGGTCCCTCAAGCTTA
65 CACGTCT-GTCACTCAAGATTA
* * *
122726 TCATTAAGGAACCCCTACATATCACGTTAGTCCCTCTAATTGTCATCAAGGAACCCCTACATATC
1 TCATCAAGGAACCCCTAAATATCACGTTGGTCCCTCTAATTGTCATCAAGGAACCCCTACATATC
122791 ACGTCTGTCACTCAAGATTA
66 ACGTCTGTCACTCAAGATTA
*
122811 TCATCAAGGAACCCCTAAATATTACGTTGGTCC
1 TCATCAAGGAACCCCTAAATATCACGTTGGTCC
122844 ATCAAGCTTG
Statistics
Matches: 106, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
85 102 0.96
86 4 0.04
ACGTcount: A:0.29, C:0.30, G:0.13, T:0.28
Consensus pattern (85 bp):
TCATCAAGGAACCCCTAAATATCACGTTGGTCCCTCTAATTGTCATCAAGGAACCCCTACATATC
ACGTCTGTCACTCAAGATTA
Found at i:124515 original size:9 final size:8
Alignment explanation
Indices: 124501--124609 Score: 60
Period size: 8 Copynumber: 12.8 Consensus size: 8
124491 TCTCTCTCAT
124501 TTTTATTTC
1 TTTT-TTTC
124510 TTTTATTTC
1 TTTT-TTTC
124519 TTTTTTCTGC
1 TTTTTT-T-C
124529 TTTTTTTC
1 TTTTTTTC
124537 TTTTTTT-
1 TTTTTTTC
**
124544 TCCTTTTC
1 TTTTTTTC
*
124552 TATATTTTCC
1 T-T-TTTTTC
124562 TTTTTTT-
1 TTTTTTTC
**
124569 TCCTTTTC
1 TTTTTTTC
124577 TATATTTTTCC
1 T-T-TTTTT-C
124588 TTTTTTTC
1 TTTTTTTC
*
124596 TATTTTTC
1 TTTTTTTC
*
124604 CTTTTT
1 TTTTTT
124610 CTATATCATT
Statistics
Matches: 78, Mismatches: 13, Indels: 19
0.71 0.12 0.17
Matches are distributed among these distances:
7 10 0.13
8 28 0.36
9 21 0.27
10 17 0.22
11 2 0.03
ACGTcount: A:0.06, C:0.17, G:0.01, T:0.76
Consensus pattern (8 bp):
TTTTTTTC
Found at i:124522 original size:18 final size:17
Alignment explanation
Indices: 124501--124609 Score: 62
Period size: 17 Copynumber: 6.3 Consensus size: 17
124491 TCTCTCTCAT
124501 TTTTATTTCTTTTATTT-C
1 TTTT-TTTCTTTT-TTTCC
*
124519 TTTTTTCTGCTTTTTTTCT
1 TTTTTT-T-CTTTTTTTCC
* * *
124538 TTTTTTTCCTTTTCT-A
1 TTTTTTTCTTTTTTTCC
* *
124554 TATTTTCCTTTTTTTTCC
1 TTTTTTTC-TTTTTTTCC
* * *
124572 -TTTTCTATATTTTTCC
1 TTTTTTTCTTTTTTTCC
*
124588 TTTTTTTCTATTTTTCC
1 TTTTTTTCTTTTTTTCC
124605 TTTTT
1 TTTTT
124610 CTATATCATT
Statistics
Matches: 69, Mismatches: 16, Indels: 13
0.70 0.16 0.13
Matches are distributed among these distances:
16 14 0.20
17 35 0.51
18 9 0.13
19 11 0.16
ACGTcount: A:0.06, C:0.17, G:0.01, T:0.76
Consensus pattern (17 bp):
TTTTTTTCTTTTTTTCC
Found at i:124533 original size:11 final size:9
Alignment explanation
Indices: 124500--124609 Score: 53
Period size: 9 Copynumber: 11.6 Consensus size: 9
124490 TTCTCTCTCA
124500 TTTTTATTTC
1 TTTTT-TTTC
*
124510 TTTTATTTC
1 TTTTTTTTC
*
124519 TTTTTTCTGC
1 TTTTTT-TTC
124529 -TTTTTTTC
1 TTTTTTTTC
124537 TTTTTTTTCC
1 TTTTTTTT-C
* * *
124547 TTTTCTATA
1 TTTTTTTTC
124556 TTTTCCTTTT-
1 TTTT--TTTTC
124566 TTTTCCTTTTC
1 TTTT--TTTTC
*
124577 TATATTTTTC
1 T-TTTTTTTC
*
124587 CTTTTTTTC
1 TTTTTTTTC
* *
124596 TATTTTTCC
1 TTTTTTTTC
124605 TTTTT
1 TTTTT
124610 CTATATCATT
Statistics
Matches: 77, Mismatches: 16, Indels: 15
0.71 0.15 0.14
Matches are distributed among these distances:
8 2 0.03
9 42 0.55
10 28 0.36
11 3 0.04
12 2 0.03
ACGTcount: A:0.06, C:0.16, G:0.01, T:0.76
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:124559 original size:26 final size:26
Alignment explanation
Indices: 124463--124594 Score: 115
Period size: 25 Copynumber: 4.9 Consensus size: 26
124453 TGTTGGATTT
* *
124463 TTTTCTTTATTCTTTTCTTCTTTTTCC
1 TTTTCTATATT-TTTTCTTTTTTTTCC
* * *
124490 TTCTCTCTCATTTTTATTTCTTTTATTTCTT
1 TT-T-TCT-ATATTT-TTTCTTTTTTTTC-C
*
124521 TTTTCTGCT-TTTTTTCTTTTTTTTCC
1 TTTTCT-ATATTTTTTCTTTTTTTTCC
*
124547 TTTTCTATA-TTTTCCTTTTTTTTCC
1 TTTTCTATATTTTTTCTTTTTTTTCC
*
124572 TTTTCTATATTTTTCCTTTTTTT
1 TTTTCTATATTTTTTCTTTTTTT
124595 CTATTTTTCC
Statistics
Matches: 87, Mismatches: 11, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
25 25 0.29
26 19 0.22
27 14 0.16
28 4 0.05
29 8 0.09
30 15 0.17
31 2 0.02
ACGTcount: A:0.06, C:0.19, G:0.01, T:0.74
Consensus pattern (26 bp):
TTTTCTATATTTTTTCTTTTTTTTCC
Found at i:124575 original size:16 final size:16
Alignment explanation
Indices: 124540--124615 Score: 67
Period size: 17 Copynumber: 5.1 Consensus size: 16
124530 TTTTTTCTTT
124540 TTTTTCCTTTTCTATA
1 TTTTTCCTTTTCTATA
124556 -TTTTCC---T-T-T-
1 TTTTTCCTTTTCTATA
124565 TTTTTCCTTTTCTATA
1 TTTTTCCTTTTCTATA
* *
124581 TTTTTCCTTTTTTTCTA
1 TTTTTCC-TTTTCTATA
124598 TTTTTCCTTTTTCTATA
1 TTTTTCC-TTTTCTATA
124615 T
1 T
124616 CATTTCTTCT
Statistics
Matches: 48, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
10 7 0.15
11 1 0.02
12 1 0.02
13 1 0.02
14 1 0.02
15 7 0.15
16 7 0.15
17 23 0.48
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTCCTTTTCTATA
Found at i:124584 original size:17 final size:17
Alignment explanation
Indices: 124564--124615 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
124554 TATTTTCCTT
124564 TTTTTTCCTTTTCTATA
1 TTTTTTCCTTTTCTATA
* *
124581 -TTTTTCCTTTT-TTTC
1 TTTTTTCCTTTTCTATA
124596 TATTTTTCCTTTTTCTATA
1 T-TTTTTCC-TTTTCTATA
124615 T
1 T
124616 CATTTCTTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
15 2 0.07
16 11 0.41
17 7 0.26
18 4 0.15
19 3 0.11
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTTTCCTTTTCTATA
Found at i:124601 original size:26 final size:26
Alignment explanation
Indices: 124531--124601 Score: 94
Period size: 26 Copynumber: 2.8 Consensus size: 26
124521 TTTTCTGCTT
*
124531 TTTTTCTTTTTTTTC-CTTTTCTATA
1 TTTTTCCTTTTTTTCTCTTTTCTATA
124556 -TTTTCCTTTTTTT-TCCTTTTCTATA
1 TTTTTCCTTTTTTTCT-CTTTTCTATA
*
124581 TTTTTCCTTTTTTTCTATTTT
1 TTTTTCCTTTTTTTCTCTTTT
124602 TCCTTTTTCT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
24 12 0.30
25 10 0.25
26 17 0.43
27 1 0.03
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (26 bp):
TTTTTCCTTTTTTTCTCTTTTCTATA
Found at i:124629 original size:34 final size:33
Alignment explanation
Indices: 124565--124630 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 33
124555 ATTTTCCTTT
* *
124565 TTTTTCCTTTTCTATATTTTTCCTTTTTTTCTA
1 TTTTTCCTTTTCTATATATTTCCTTCTTTTCTA
124598 TTTTTCCTTTTTCTATATCATTT-CTTCTTTTCT
1 TTTTTCC-TTTTCTATAT-ATTTCCTTCTTTTCT
124631 TTATGTTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 7 0.24
34 19 0.66
35 3 0.10
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.71
Consensus pattern (33 bp):
TTTTTCCTTTTCTATATATTTCCTTCTTTTCTA
Found at i:125015 original size:53 final size:53
Alignment explanation
Indices: 124935--125043 Score: 200
Period size: 53 Copynumber: 2.1 Consensus size: 53
124925 AAGTCTTTGT
* *
124935 AAAAGAGGTATCCTTAGGGGGACGAGTATTCAGGATTAACCTTATTTACATGA
1 AAAAGAGGTATCCTCAGGGGGAAGAGTATTCAGGATTAACCTTATTTACATGA
124988 AAAAGAGGTATCCTCAGGGGGAAGAGTATTCAGGATTAACCTTATTTACATGA
1 AAAAGAGGTATCCTCAGGGGGAAGAGTATTCAGGATTAACCTTATTTACATGA
125041 AAA
1 AAA
125044 CAATGTAATT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.27
Consensus pattern (53 bp):
AAAAGAGGTATCCTCAGGGGGAAGAGTATTCAGGATTAACCTTATTTACATGA
Found at i:126985 original size:21 final size:20
Alignment explanation
Indices: 126959--127027 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 20
126949 GAACCTATCA
126959 TCCCGAAGGATGTCATCTGTG
1 TCCCGAAGGATGTCATCT-TG
*
126980 TCCCGAAGGACT-T-A--TTA
1 TCCCGAAGGA-TGTCATCTTG
*
126997 TCCCGAAGGTTGTCATCTATG
1 TCCCGAAGGATGTCATCT-TG
127018 TCCCGAAGGA
1 TCCCGAAGGA
127028 CCTATCATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
16 1 0.03
17 11 0.29
18 2 0.05
20 2 0.05
21 21 0.55
22 1 0.03
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.28
Consensus pattern (20 bp):
TCCCGAAGGATGTCATCTTG
Found at i:126987 original size:38 final size:38
Alignment explanation
Indices: 126935--127035 Score: 139
Period size: 38 Copynumber: 2.7 Consensus size: 38
126925 GGCATGTGAA
* * *
126935 ATCTGTATCTCGAAGAACCTATCATCCCGAAGGATGTC
1 ATCTGTGTCCCGAAGGACCTATCATCCCGAAGGATGTC
* * *
126973 ATCTGTGTCCCGAAGGACTTATTATCCCGAAGGTTGTC
1 ATCTGTGTCCCGAAGGACCTATCATCCCGAAGGATGTC
*
127011 ATCTATGTCCCGAAGGACCTATCAT
1 ATCTGTGTCCCGAAGGACCTATCAT
127036 ATATCCCGAA
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.29
Consensus pattern (38 bp):
ATCTGTGTCCCGAAGGACCTATCATCCCGAAGGATGTC
Found at i:128805 original size:31 final size:31
Alignment explanation
Indices: 128769--128843 Score: 132
Period size: 31 Copynumber: 2.4 Consensus size: 31
128759 CTAAATTACC
128769 AATTTACCCTTAAAATTAAAATATCTATACT
1 AATTTACCCTTAAAATTAAAATATCTATACT
*
128800 AATTTACCCTTGAAATTAAAATATCTATACT
1 AATTTACCCTTAAAATTAAAATATCTATACT
*
128831 GATTTACCCTTAA
1 AATTTACCCTTAA
128844 TGAACTTGAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.39
Consensus pattern (31 bp):
AATTTACCCTTAAAATTAAAATATCTATACT
Found at i:131772 original size:22 final size:22
Alignment explanation
Indices: 131747--131831 Score: 70
Period size: 22 Copynumber: 4.0 Consensus size: 22
131737 TTAAATTTAG
131747 AATTAAAACTATAAAATAAAAC
1 AATTAAAACTATAAAATAAAAC
* *
131769 AATTAAAA--ATCAACT--AAC
1 AATTAAAACTATAAAATAAAAC
* * *
131787 AATTAAAACAAAAGATAATAAAAA
1 AATTAAAACTATA-A-AATAAAAC
*
131811 AATTAAAAATATAAAATAAAA
1 AATTAAAACTATAAAATAAAA
131832 TAAAGACATA
Statistics
Matches: 48, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
18 11 0.23
20 6 0.12
21 1 0.02
22 17 0.35
23 1 0.02
24 12 0.25
ACGTcount: A:0.71, C:0.07, G:0.01, T:0.21
Consensus pattern (22 bp):
AATTAAAACTATAAAATAAAAC
Found at i:135511 original size:2 final size:2
Alignment explanation
Indices: 135504--135537 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
135494 TCAACACAGG
135504 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
135538 AAGCATTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:135793 original size:26 final size:26
Alignment explanation
Indices: 135757--135810 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
135747 ATATGTTAAT
135757 GTGATAATATGACACATGACGTATAA
1 GTGATAATATGACACATGACGTATAA
**
135783 GTGATAATATGACACATGTTGTATAA
1 GTGATAATATGACACATGACGTATAA
135809 GT
1 GT
135811 CATGATACGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.31
Consensus pattern (26 bp):
GTGATAATATGACACATGACGTATAA
Found at i:135822 original size:26 final size:26
Alignment explanation
Indices: 135760--135822 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
135750 TGTTAATGTG
* *
135760 ATAATATGACACATGACGTATAAGTG
1 ATAATACGACACATGACGTATAAGTC
* **
135786 ATAATATGACACATGTTGTATAAGTC
1 ATAATACGACACATGACGTATAAGTC
*
135812 ATGATACGACA
1 ATAATACGACA
135823 TTTTAATATT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (26 bp):
ATAATACGACACATGACGTATAAGTC
Found at i:136849 original size:4 final size:4
Alignment explanation
Indices: 136840--136876 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
136830 AAAAAATATA
*
136840 TTAT TTAT TTAT TTAT TTA- TTA- TTAT TAAT TTAT TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA
136877 CATTTGTGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 6 0.20
4 24 0.80
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (4 bp):
TTAT
Found at i:137955 original size:16 final size:16
Alignment explanation
Indices: 137907--137956 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
137897 GAGAGAGTCC
*
137907 AAAGAAAAAGGAAAAG
1 AAAGAAAAAGGATAAG
* *
137923 -AAG-AAATGAGATTAG
1 AAAGAAAAAG-GATAAG
137938 AAAGAAAAAGGATAAG
1 AAAGAAAAAGGATAAG
137954 AAA
1 AAA
137957 TTAGGTATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 6
0.70 0.14 0.16
Matches are distributed among these distances:
14 4 0.15
15 7 0.27
16 11 0.42
17 4 0.15
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (16 bp):
AAAGAAAAAGGATAAG
Found at i:138909 original size:2 final size:2
Alignment explanation
Indices: 138902--138937 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
138892 TAAATGGATC
138902 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
138938 GACTTGAGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:139157 original size:24 final size:24
Alignment explanation
Indices: 139125--139175 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
139115 GGGTTTTGAT
139125 TGAGATTAAAGTAGTTGGAAACCC
1 TGAGATTAAAGTAGTTGGAAACCC
139149 TGAGATTAAAGTAGTTGGAAACCC
1 TGAGATTAAAGTAGTTGGAAACCC
139173 TGA
1 TGA
139176 TCAGGATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.25
Consensus pattern (24 bp):
TGAGATTAAAGTAGTTGGAAACCC
Found at i:139280 original size:29 final size:28
Alignment explanation
Indices: 139248--139341 Score: 100
Period size: 29 Copynumber: 3.2 Consensus size: 28
139238 TAAGTACTTG
* *
139248 AAGTATTTTTTAGTCCAAATAAGTATCTA
1 AAGTATTTTTT-GTCAAAATAGGTATCTA
139277 AAGTTATTTTTTGTCAAAATAGGTA-CTCA
1 AAG-TATTTTTTGTCAAAATAGGTATCT-A
* * *
139306 AAGTATTTCTTGGTCAAAATGGGTATTTA
1 AAGTATTT-TTTGTCAAAATAGGTATCTA
139335 AAGTATT
1 AAGTATT
139342 CAAATTTTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
28 7 0.12
29 40 0.71
30 9 0.16
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (28 bp):
AAGTATTTTTTGTCAAAATAGGTATCTA
Found at i:139378 original size:24 final size:23
Alignment explanation
Indices: 139329--139383 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
139319 TCAAAATGGG
* * *
139329 TATTTAAAGTATTCAAATTTTTTT
1 TATTT-AAGTATTAAAATATTCTT
139353 TATTTAAGTATATAAAATATTCTT
1 TATTTAAGTAT-TAAAATATTCTT
*
139377 TAATTAA
1 TATTTAA
139384 TGCATATGTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 6 0.23
24 20 0.77
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (23 bp):
TATTTAAGTATTAAAATATTCTT
Found at i:139496 original size:31 final size:28
Alignment explanation
Indices: 139424--139524 Score: 85
Period size: 28 Copynumber: 3.5 Consensus size: 28
139414 GAAAAAGTTT
* * *** *
139424 AAATAATTTACGTATCTATTTTGGCATA
1 AAATAATTTAGGTATCTAGTTTAATAAA
*
139452 AAATATTTTAGGTATCTAGTTTAATTAAA
1 AAATAATTTAGGTATCTAGTTTAA-TAAA
* * *
139481 AAGATAACTTTAGGTATTTATTTTGATAAA
1 AA-ATAA-TTTAGGTATCTAGTTTAATAAA
139511 AAATAATTTAGGTA
1 AAATAATTTAGGTA
139525 CTTGAATGAA
Statistics
Matches: 59, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
28 27 0.46
29 8 0.14
30 9 0.15
31 15 0.25
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.43
Consensus pattern (28 bp):
AAATAATTTAGGTATCTAGTTTAATAAA
Found at i:142169 original size:20 final size:20
Alignment explanation
Indices: 142144--142183 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
142134 ATCTTTTGTC
*
142144 TTTGTAGATCCTGTAGATAA
1 TTTGTAGATCCTATAGATAA
142164 TTTGTAGATCCTATAGATAA
1 TTTGTAGATCCTATAGATAA
142184 AATAGGGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (20 bp):
TTTGTAGATCCTATAGATAA
Found at i:143783 original size:13 final size:13
Alignment explanation
Indices: 143765--143813 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
143755 AAGAGGATTG
143765 CACAAAGAATGCA
1 CACAAAGAATGCA
*
143778 CACAAAGAATGCG
1 CACAAAGAATGCA
* *
143791 TACAAAGAATGTA
1 CACAAAGAATGCA
*
143804 CAAAAAGAAT
1 CACAAAGAAT
143814 TGGATCCTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.55, C:0.16, G:0.16, T:0.12
Consensus pattern (13 bp):
CACAAAGAATGCA
Found at i:145272 original size:42 final size:44
Alignment explanation
Indices: 145217--145321 Score: 133
Period size: 43 Copynumber: 2.4 Consensus size: 44
145207 TAAAAATCAA
* *
145217 TCGGGTTCGGGGTCGGGTCGGGTCG-GATTTTTTAAGTTTGATAT
1 TCGGG-TCAGGGTCGGGTCGGGTCGAGATTTTTTAAGTGTGATAT
* *
145261 TCGGGTC-GGGTCTGGTCGGGTCGAGTTTTTTTAAGTGTGATAT
1 TCGGGTCAGGGTCGGGTCGGGTCGAGATTTTTTAAGTGTGATAT
* *
145304 TCAGGTCAGGTTCGGGTC
1 TCGGGTCAGGGTCGGGTC
145322 TGGTTTTTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
42 15 0.28
43 25 0.47
44 13 0.25
ACGTcount: A:0.11, C:0.13, G:0.38, T:0.37
Consensus pattern (44 bp):
TCGGGTCAGGGTCGGGTCGGGTCGAGATTTTTTAAGTGTGATAT
Found at i:145471 original size:18 final size:18
Alignment explanation
Indices: 145432--145478 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
145422 CGAGTTTAGG
* *
145432 GTTTAGTGTTTAGATCAG
1 GTTTAGGGTTTAGATCAA
145450 GTTTAGGGTTTAGAT-ATA
1 GTTTAGGGTTTAGATCA-A
*
145468 GTTTAAGGTTT
1 GTTTAGGGTTT
145479 TTTAAGTTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 1 0.04
18 24 0.96
ACGTcount: A:0.23, C:0.02, G:0.28, T:0.47
Consensus pattern (18 bp):
GTTTAGGGTTTAGATCAA
Found at i:152178 original size:43 final size:47
Alignment explanation
Indices: 152115--152232 Score: 147
Period size: 47 Copynumber: 2.6 Consensus size: 47
152105 CTAGATCTCT
*
152115 TCATCACGTAGG-ATTCGTGTCA-C-T-C-TCAGATAATCAGTAGTCC
1 TCATCACGTAGGAATT-GTGTCATCATCCTTCAGATAAACAGTAGTCC
* * *
152158 TCATCACGTAGGAACTGTGTCATCATCCTTTAGATAAACAGTTGTCC
1 TCATCACGTAGGAATTGTGTCATCATCCTTCAGATAAACAGTAGTCC
*
152205 TCATCACGTAGGAATTGTGTTATCATCC
1 TCATCACGTAGGAATTGTGTCATCATCC
152233 CTAGACGACC
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
43 18 0.28
44 3 0.05
45 1 0.02
46 1 0.02
47 41 0.64
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (47 bp):
TCATCACGTAGGAATTGTGTCATCATCCTTCAGATAAACAGTAGTCC
Found at i:152467 original size:3 final size:3
Alignment explanation
Indices: 152461--152504 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
152451 AATAATAATA
* * *
152461 ATT ATT ATT ATT ATT ATC ATTT ATT ATA ATA ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT A
152505 CATGTTTACA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
3 34 0.94
4 2 0.06
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:153421 original size:12 final size:13
Alignment explanation
Indices: 153404--153440 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
153394 AATGTGATAT
153404 ATATATATATA-G
1 ATATATATATAGG
153416 ATATATATATAGG
1 ATATATATATAGG
153429 ATAT-TA-ATAGG
1 ATATATATATAGG
153440 A
1 A
153441 AAACATCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 6 0.25
12 13 0.54
13 5 0.21
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.38
Consensus pattern (13 bp):
ATATATATATAGG
Found at i:153904 original size:30 final size:31
Alignment explanation
Indices: 153870--153957 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 31
153860 TCTATTAATA
*
153870 CTATTTTAATCCTTTACATTTTTG-TTTGTG
1 CTATTTTAATCCTTTAAATTTTTGTTTTGTG
** * *
153900 CTATTTTGGTACTTTAAATTTTTGTTTTTTG
1 CTATTTTAATCCTTTAAATTTTTGTTTTGTG
* * *
153931 CTA-TTTAATCCCTTAAGTTTCTGTTTT
1 CTATTTTAATCCTTTAAATTTTTGTTTT
153958 TCTCTTGCAG
Statistics
Matches: 46, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
30 38 0.83
31 8 0.17
ACGTcount: A:0.17, C:0.12, G:0.10, T:0.60
Consensus pattern (31 bp):
CTATTTTAATCCTTTAAATTTTTGTTTTGTG
Found at i:158203 original size:11 final size:11
Alignment explanation
Indices: 158187--158214 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
158177 CCTGAACTGA
158187 AGCTCGTGAGC
1 AGCTCGTGAGC
158198 AGCTCGTGAGC
1 AGCTCGTGAGC
158209 AGCTCG
1 AGCTCG
158215 AAACGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.18, C:0.29, G:0.36, T:0.18
Consensus pattern (11 bp):
AGCTCGTGAGC
Found at i:159511 original size:180 final size:184
Alignment explanation
Indices: 159173--159540 Score: 665
Period size: 180 Copynumber: 2.0 Consensus size: 184
159163 TAAAATTTAA
*
159173 AACGTTCATCATCTTTCATTCACCATTTACAAATATACGTTTAAAACATTACAAAATTCAATCAT
1 AACGTGCATCATCTTTCATTCACCATTTACAAATATACGTTTAAAACATTACAAAATT--ATCAT
159238 ATGTTTTTACAAAACTGATTTAAAACATATCGTATTCAAACCCTTATTTACATGCCAACCACTAT
64 ATGTTTTTACAAAACTGATTTAAAACATATCGTATTCAAACCCTTATTTACATGCCAACCACTAT
159303 CCTTATTACAAATACATACTATACATTTCTTTTCTGATATGATCATTGTAAAGGAG
129 CCTTATTACAAATACATACTATACATTTCTTTTCTGATATGATCATTGTAAAGGAG
159359 AACGTGCATCATCTTTCATTCACCA-TTACAAATATACGTTTAAAACATTACAAAA-T-TCATAT
1 AACGTGCATCATCTTTCATTCACCATTTACAAATATACGTTTAAAACATTACAAAATTATCATAT
159421 GTTTTTACAAAACTGATTTAAAACATATCGTATTC-AACCCTTATTTACATGCCAACCA-TATCC
66 GTTTTTACAAAACTGATTTAAAACATATCGTATTCAAACCCTTATTTACATGCCAACCACTATCC
159484 TTATTACAAAATACATACTATACATTTCTTTTCTGATATGATCATTGTAAAGGAG
131 TTATTAC-AAATACATACTATACATTTCTTTTCTGATATGATCATTGTAAAGGAG
159539 AA
1 AA
159541 ACTGACTTGT
Statistics
Matches: 180, Mismatches: 1, Indels: 8
0.95 0.01 0.04
Matches are distributed among these distances:
179 12 0.07
180 72 0.40
181 41 0.23
184 1 0.01
185 30 0.17
186 24 0.13
ACGTcount: A:0.38, C:0.20, G:0.07, T:0.36
Consensus pattern (184 bp):
AACGTGCATCATCTTTCATTCACCATTTACAAATATACGTTTAAAACATTACAAAATTATCATAT
GTTTTTACAAAACTGATTTAAAACATATCGTATTCAAACCCTTATTTACATGCCAACCACTATCC
TTATTACAAATACATACTATACATTTCTTTTCTGATATGATCATTGTAAAGGAG
Found at i:160009 original size:148 final size:155
Alignment explanation
Indices: 159826--160128 Score: 557
Period size: 148 Copynumber: 2.0 Consensus size: 155
159816 TATTAAACAT
159826 TTCCATATATATTATAGAACACATATATCATTTCATAACAAAACACACATAACATCATACAATTC
1 TTCCATATATATTATAGAACACATATATCATTTCATAACAAAACACACATAACATCATACAATTC
159891 ATGTAACATA-TTT-TATCACCAAAAGCATATACATCACATATA-TGTA-TTGTTATTGTCTCTT
66 ATGTAACATATTTTATATCACCAAAAGCATATACATCACATATATTGTATTTGTTATTGTCTCTT
159952 T-TTAGCCCGTGTACA-TTTTGAGA
131 TATTAGCCCGTGTACATTTTTGAGA
159975 TTCCATATA-ATTATAGAACACATATATCATTTCATAACAAAACACACATAACATCATACAATTC
1 TTCCATATATATTATAGAACACATATATCATTTCATAACAAAACACACATAACATCATACAATTC
160039 ATGTAACATATTTTATATCACCAAAAGCATATACATCACATATATTGTATTTGTTATTGTCTCTT
66 ATGTAACATATTTTATATCACCAAAAGCATATACATCACATATATTGTATTTGTTATTGTCTCTT
160104 TATTAGCCCGTGTACATTTTTGAGA
131 TATTAGCCCGTGTACATTTTTGAGA
160129 ACTTAAGGTA
Statistics
Matches: 148, Mismatches: 0, Indels: 7
0.95 0.00 0.05
Matches are distributed among these distances:
148 65 0.44
149 12 0.08
150 29 0.20
151 4 0.03
152 16 0.11
153 14 0.09
154 8 0.05
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.37
Consensus pattern (155 bp):
TTCCATATATATTATAGAACACATATATCATTTCATAACAAAACACACATAACATCATACAATTC
ATGTAACATATTTTATATCACCAAAAGCATATACATCACATATATTGTATTTGTTATTGTCTCTT
TATTAGCCCGTGTACATTTTTGAGA
Found at i:162525 original size:17 final size:16
Alignment explanation
Indices: 162505--162538 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
162495 AAAGAACAGT
162505 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
162522 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
162538 A
1 A
162539 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:166361 original size:20 final size:21
Alignment explanation
Indices: 166338--166381 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
166328 GAGAAAAGGT
*
166338 AAAAGTTAA-AATGAAAGAGA
1 AAAAATTAATAATGAAAGAGA
*
166358 AAAAATTAATAATGAAAGATA
1 AAAAATTAATAATGAAAGAGA
166379 AAA
1 AAA
166382 GAAAAAGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.18
Consensus pattern (21 bp):
AAAAATTAATAATGAAAGAGA
Found at i:172543 original size:17 final size:16
Alignment explanation
Indices: 172523--172556 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
172513 AAAGAACAGT
172523 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
172540 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
172556 A
1 A
172557 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:183246 original size:21 final size:20
Alignment explanation
Indices: 183217--183255 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
183207 GCAAACTGGA
183217 ATAAAAGTATCGATACTTAT
1 ATAAAAGTATCGATACTTAT
183237 ATAATAAGTATCGATACTT
1 ATAA-AAGTATCGATACTT
183256 TATGTTTACG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (20 bp):
ATAAAAGTATCGATACTTAT
Found at i:183327 original size:202 final size:199
Alignment explanation
Indices: 182889--183555 Score: 880
Period size: 200 Copynumber: 3.3 Consensus size: 199
182879 GTTCAATTGG
* *
182889 TTTTACCGTTTACATTGTAAATTTACTTATAACTTTAAAGTAATCGGTTTCGAAATTCCATGTAT
1 TTTTACCGTTTACATTGTAAATTTACCTATAACTTTAAAGTAATCGGTTTCGAAATT-CAAGTAT
* * * *
182954 CGATACTTTATACATGTGTATCGATACTTTGTGCCTGCAAATTG-TTGAGAAGCATATTGGACTA
65 CGATACTTTATACATGTGTATCAATACTTTGTGCGTGCAAATTGTTTGAGAAGCATACTGGAATA
* * * * * *
183018 AAAGTATCGATACCTATACAA-AACGTATCAATACTTGATGTTTACGTCTATTATCATTAAATCG
130 AAAGTATCGATACTTATATAATAA-GTATCGATACTTTATGTTTACGCCTATTATCATTAAACCG
*
183082 GTAGAC
194 GTAGAT
* * *
183088 TTTCACTGTTTACATTGTAAATTTACCTATAACTTTAAAGTAATCGGTTTCGAAATTCAGCGTAT
1 TTTTACCGTTTACATTGTAAATTTACCTATAACTTTAAAGTAATCGGTTTCGAAATTCA-AGTAT
* * * *
183153 CGATACTTTATACATGTGTATCAATACTTTTTTTGCGTGTAAATTGTTTGAGATGCAAACTGGAA
65 CGATACTTTATACATGTGTATCAATAC--TTTGTGCGTGCAAATTGTTTGAGAAGCATACTGGAA
183218 TAAAAGTATCGATACTTATATAATAAGTATCGATACTTTATGTTTACGCCTATTATCATTAAACC
128 TAAAAGTATCGATACTTATATAATAAGTATCGATACTTTATGTTTACGCCTATTATCATTAAACC
183283 GGTA-ATT
193 GGTAGA-T
* * * * *
183290 TTTTACCGTTTACATTGTAAATTTACCTATTACTTTAAAGAAATAGGTTTCGAAATTATAATTAT
1 TTTTACCGTTTACATTGTAAATTTACCTATAACTTTAAAGTAATCGGTTTCGAAATT-CAAGTAT
*
183355 CGATACTTGTTATACA--TGTATCAATACTTTGTGCGTGCAAATTGTTTGAGACGCATACTGGAA
65 CGATAC-T-TTATACATGTGTATCAATACTTTGTGCGTGCAAATTGTTTGAGAAGCATACTGGAA
* *
183418 TAAAAGTATCGATACTTATATAATAAGTATTGATACGTTATGTTTACGCCTATTATCATTAAACC
128 TAAAAGTATCGATACTTATATAATAAGTATCGATACTTTATGTTTACGCCTATTATCATTAAACC
*
183483 AGTAGAT
193 GGTAGAT
* * * *
183490 TTTTACCGTTTATATTGTAAATTTAAGC-ATTACTTTAAAGTAATAC-GTTTCAAAATTCTAAGT
1 TTTTACCGTTTACATTGTAAATTT-ACCTATAACTTTAAAGTAAT-CGGTTTCGAAATTC-AAGT
183553 ATC
63 ATC
183556 AAAACTTTGT
Statistics
Matches: 414, Mismatches: 41, Indels: 25
0.86 0.09 0.05
Matches are distributed among these distances:
198 2 0.00
199 84 0.20
200 153 0.37
201 18 0.04
202 146 0.35
203 4 0.01
204 7 0.02
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (199 bp):
TTTTACCGTTTACATTGTAAATTTACCTATAACTTTAAAGTAATCGGTTTCGAAATTCAAGTATC
GATACTTTATACATGTGTATCAATACTTTGTGCGTGCAAATTGTTTGAGAAGCATACTGGAATAA
AAGTATCGATACTTATATAATAAGTATCGATACTTTATGTTTACGCCTATTATCATTAAACCGGT
AGAT
Found at i:183381 original size:21 final size:19
Alignment explanation
Indices: 183345--183383 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
183335 GGTTTCGAAA
*
183345 TTATAATTATCGATACTTG
1 TTATAATTATCAATACTTG
183364 TTATACATGTATCAATACTT
1 TTATA-AT-TATCAATACTT
183384 TGTGCGTGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (19 bp):
TTATAATTATCAATACTTG
Found at i:183440 original size:20 final size:22
Alignment explanation
Indices: 183417--183458 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
183407 GCATACTGGA
183417 ATAA-AAGTATCGATAC-TTAT
1 ATAATAAGTATCGATACGTTAT
*
183437 ATAATAAGTATTGATACGTTAT
1 ATAATAAGTATCGATACGTTAT
183459 GTTTACGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 11 0.58
22 4 0.21
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (22 bp):
ATAATAAGTATCGATACGTTAT
Found at i:185025 original size:6 final size:6
Alignment explanation
Indices: 185016--185062 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
185006 AGTGGAGCTT
* * * *
185016 AAATTG AAATTG AAATTG AAATTC AAATTA AAATTC AACTTG AAATT
1 AAATTG AAATTG AAATTG AAATTG AAATTG AAATTG AAATTG AAATT
185063 AAAAACAACA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (6 bp):
AAATTG
Found at i:185033 original size:12 final size:12
Alignment explanation
Indices: 185016--185062 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
185006 AGTGGAGCTT
*
185016 AAATTGAAATTG
1 AAATTGAAATTC
185028 AAATTGAAATTC
1 AAATTGAAATTC
*
185040 AAATTAAAATTC
1 AAATTGAAATTC
*
185052 AACTTGAAATT
1 AAATTGAAATT
185063 AAAAACAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (12 bp):
AAATTGAAATTC
Found at i:185043 original size:18 final size:18
Alignment explanation
Indices: 185016--185066 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
185006 AGTGGAGCTT
* *
185016 AAATTGAAATTGAAATTG
1 AAATTGAAATTAAAATTC
*
185034 AAATTCAAATTAAAATTC
1 AAATTGAAATTAAAATTC
*
185052 AACTTGAAATTAAAA
1 AAATTGAAATTAAAA
185067 ACAACATAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.55, C:0.06, G:0.08, T:0.31
Consensus pattern (18 bp):
AAATTGAAATTAAAATTC
Found at i:190717 original size:14 final size:14
Alignment explanation
Indices: 190694--190730 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
190684 TATCAAAAAC
*
190694 CCTAAACCCATAAA
1 CCTAACCCCATAAA
190708 CCTAACCCCATAAA
1 CCTAACCCCATAAA
190722 CCTAACCCC
1 CCTAACCCC
190731 TATTTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.41, C:0.46, G:0.00, T:0.14
Consensus pattern (14 bp):
CCTAACCCCATAAA
Found at i:191390 original size:196 final size:198
Alignment explanation
Indices: 191020--191484 Score: 507
Period size: 200 Copynumber: 2.3 Consensus size: 198
191010 CATTTTTTAT
* ** * * * *
191020 TTCTTTTCAATTCCTAAAGTACAAATACTATGTTACATATACTTATAAAAGTATGGATAC-CA-T
1 TTCTTTTAAATTCCTAAAGTACTGATACTTTGATACATATACTTATAAAAGTATCGATACAAATT
* * * *
191083 CAA-CATATCCAGTAGCGCTTTACCAGTTTTGTCATATTGAAACTGGTTTTTATCAAATTTCAAT
66 CAACCATATCCAGTAGCGCTTTACCAGTTTTGTCAAACTGAAACCGGTTTTTATCAAATTTCAAC
* * *
191147 ATGTTATATTGTCATGTATCGATACATGTGTCTAAGGTATCAATACTTTATAGGC-GCTATTATT
131 ATGTTATATTGTCATGTATCGATACATGTGTCTAAGGTATCAATACTTTAGAGACTCCT-TTATT
191211 GCAA
195 GCAA
* * *
191215 TTCTTTTAAATTCCTAAAGTACTGATAATTTGGTGCATATACTTATAAAAGTATCGATACAAATG
1 TTCTTTTAAATTCCTAAAGTACTGATACTTTGATACATATACTTATAAAAGTATCGATACAAAT-
* * * *** *
191280 TCAACCAT-TCCGGTATCTCTTTATTGGTTTTGTCAAACT-AAACCGG-TTTTGTCAAACTTT-A
65 TCAACCATATCCAGTAGCGCTTTACCAGTTTTGTCAAACTGAAACCGGTTTTTATCAAA-TTTCA
* *
191341 ACATGTTATATTGTCATGTATCGATACATGTGTGTAAGGTATTAATACTTTAGAGACATTTTCCT
129 ACATGTTATATTGTCATGTATCGATACATGTGTCTAAGGTATCAATACTTTAGAGAC----TCCT
* * *
191406 TTTTTTCAT
190 TTATTGCAA
* *
191415 TTCTTTTAAATTCCTACAA-TACTGATACTTTGATACATATATTTATAAATGTATCGATACAAAT
1 TTCTTTTAAATTCCTA-AAGTACTGATACTTTGATACATATACTTATAAAAGTATCGATACAAA-
191479 TTCAAC
64 TTCAAC
191485 AATTTCAACA
Statistics
Matches: 225, Mismatches: 33, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
195 52 0.23
196 63 0.28
197 9 0.04
198 27 0.12
199 3 0.01
200 66 0.29
201 5 0.02
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (198 bp):
TTCTTTTAAATTCCTAAAGTACTGATACTTTGATACATATACTTATAAAAGTATCGATACAAATT
CAACCATATCCAGTAGCGCTTTACCAGTTTTGTCAAACTGAAACCGGTTTTTATCAAATTTCAAC
ATGTTATATTGTCATGTATCGATACATGTGTCTAAGGTATCAATACTTTAGAGACTCCTTTATTG
CAA
Found at i:191537 original size:20 final size:20
Alignment explanation
Indices: 191525--191579 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
191515 AATTGAAATA
*
191525 GGTTTTGTCAAATTTCAATC
1 GGTTTTGTCAAATTCCAATC
*
191545 GGTTTTGTCAATTTCCAATC
1 GGTTTTGTCAAATTCCAATC
*
191565 GATTTTGTCAAATTC
1 GGTTTTGTCAAATTC
191580 GTTACCTGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.24, C:0.16, G:0.15, T:0.45
Consensus pattern (20 bp):
GGTTTTGTCAAATTCCAATC
Found at i:191625 original size:20 final size:19
Alignment explanation
Indices: 191528--191625 Score: 56
Period size: 20 Copynumber: 4.9 Consensus size: 19
191518 TGAAATAGGT
* *
191528 TTTGTCAAATTTCAATCGGT
1 TTTGTCAAATTTCAA-CCGA
*
191548 TTTGTC-AATTTCCAATCGA
1 TTTGTCAAATTT-CAACCGA
* *
191567 TTTTGTCAAA-TTCGTTACCTGT
1 -TTTGTCAAATTTC--AACC-GA
**
191589 TTTGTCAAATTGAAACCAGA
1 TTTGTCAAATTTCAACC-GA
191609 TTTGTCAAATTTCAACC
1 TTTGTCAAATTTCAACC
191626 TGTTATATTA
Statistics
Matches: 58, Mismatches: 13, Indels: 14
0.68 0.15 0.16
Matches are distributed among these distances:
19 7 0.12
20 36 0.62
21 13 0.22
22 2 0.03
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.42
Consensus pattern (19 bp):
TTTGTCAAATTTCAACCGA
Found at i:193259 original size:23 final size:22
Alignment explanation
Indices: 193227--193307 Score: 74
Period size: 23 Copynumber: 3.5 Consensus size: 22
193217 TAAGGTACCA
*
193227 AAAGGTAGAGAAAAACTTGTCAT
1 AAAGGCAGAGAAAAACTTG-CAT
*
193250 AAAGGCAGAGAAAAA-TGTGCCAC
1 AAAGGCAGAGAAAAACT-TG-CAT
* * *
193273 AAAGACAGAGATAAACGTGCTAT
1 AAAGGCAGAGAAAAACTTGC-AT
193296 AAAGGCAGAGAA
1 AAAGGCAGAGAA
193308 TATGCCACAA
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
22 2 0.04
23 44 0.96
ACGTcount: A:0.49, C:0.12, G:0.25, T:0.14
Consensus pattern (22 bp):
AAAGGCAGAGAAAAACTTGCAT
Done.